Bugs item #3410220, was opened at 2011-09-15 14:51 Message generated for change (Tracker Item Submitted) made by ianlscott1 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3410220&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: File Translation Group: 2.3.x Status: Open Resolution: None Priority: 5 Private: No Submitted By: Ian Scott (ianlscott1) Assigned to: Nobody/Anonymous (nobody) Summary: 3D atom connectivity error in pdbqt Initial Comment: Ian Scott, isc...@frontier.com, Windows 7, 64-bit When converting files from smiles, mol, mol2 ,sdf into pdbqt with the generate 3D coordinates active the molecules do not form correctly. Rings are broken and strange bonds form (as viewed in PyRx or Autodock). This problem can be avoided by performing the 3D conversion as an independent step with a different file output file type (e.g. sdf to sdf) and then converting to pdbqt without selecting the generate 3D coordinates option. Therefore, the problem is most likely in the pdbqt 3D coordinate generator. A example problem smiles string: COc1cc(cc(c1OC)OC)C(C(=O)N1CCCCC1C(=O)OC(CCCc1ccccc1)CCCc1cccnc1)(F)F ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3410220&group_id=40728 ------------------------------------------------------------------------------ Doing More with Less: The Next Generation Virtual Desktop What are the key obstacles that have prevented many mid-market businesses from deploying virtual desktops? How do next-generation virtual desktops provide companies an easier-to-deploy, easier-to-manage and more affordable virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
